Figure 4.

Clustering of the NUTs and the trees in the forest of life using the classical multidimensional
scaling (CMDS) method. (a) The best two-dimensional projection of the clustering of 102 NUTs (brown squares)
in a 30-dimensional space. The 14 1:1 NUTs (corresponding to COGs consisting of 1:1
orthologs) are shown as black circles. V1, V2, variables 1 and 2, respectively. (b) The best two-dimensional projection of the clustering of the 3,789 COG trees in a
669-dimensional space. The seven clusters are color-coded and the NUTs are shown by
red circles. (c) Partitioning of the trees in each cluster between the two prokaryotic domains: blue,
archaea-only (A); green, bacteria-only (B); brown, COGs including both archaea and
bacteria (A&B). (d) Classification of the trees in each cluster by COG functional categories [41,42]: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy
transformation; D, cell division and chromosome partitioning; E, amino acid metabolism
and transport; F, nucleotide metabolism and transport; G, carbohydrate metabolism
and transport; H, coenzyme metabolism and transport; I, lipid metabolism; J, translation
and ribosome biogenesis; K, transcription; L, replication and repair; M, cell envelope
and outer membrane biogenesis; N, cell motility and secretion; O, post-translational
modification, protein turnover, chaperones; P, inorganic ion transport and metabolism;
Q, secondary metabolism; R, general functional prediction only; S, uncharacterized.
(e) The mean similarity values between the 102 NUTs and each of the seven tree clusters
in the forest of life (colors as in (b)).